[gmx-users] itp file for flavins

[Justin A. Lemkul]

On 5/15/12 5:37 PM, vijaya subramanian wrote:
> Hi
> I found all the rtp files-aminoacid.rtp,dna.rtp but not fmnr.rtp which is in
> ffgmx.rtp according to the gromacs building blocks site.
> I need to look at the fmnr.rtp file to match atom names.

Individual molecules generally do not have their own .rtp files.  The parameters 
you need are in aminoacids.rtp:

$ grep FMN g*.ff/*.rtp
gmx.ff/aminoacids.rtp:[ FMNO ]
gmx.ff/aminoacids.rtp:[ FMNR ]
gmx.ff/aminoacids.rtp:[ FMNS ]
gromos43a1.ff/aminoacids.rtp:[ FMNO ]
gromos43a1.ff/aminoacids.rtp:[ FMNS ]
gromos43a1.ff/aminoacids.rtp:[ FMNR ]
gromos43a2.ff/aminoacids.rtp:[ FMNO ]
gromos43a2.ff/aminoacids.rtp:[ FMNS ]
gromos43a2.ff/aminoacids.rtp:[ FMNR ]
gromos45a3.ff/aminoacids.rtp:[ FMNO ]
gromos45a3.ff/aminoacids.rtp:[ FMNS ]
gromos45a3.ff/aminoacids.rtp:[ FMNR ]
gromos53a5.ff/aminoacids.rtp:[ FMNO ]
gromos53a5.ff/aminoacids.rtp:[ FMNS ]
gromos53a5.ff/aminoacids.rtp:[ FMNR ]
gromos53a6.ff/aminoacids.rtp:[ FMNO ]
gromos53a6.ff/aminoacids.rtp:[ FMNS ]
gromos53a6.ff/aminoacids.rtp:[ FMNR ]

I would recommend not using gmx.ff, for reasons described in the manual.  The 
newer versions of Gromos96 are more suitable.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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